About uiuiui172

Could you please upload the transportation map of your city plus the map of your subway system?
And as far as buses go, Maxis's failure to create a bus route system makes the game much more difficult and causes congestion, buses in real life typically stick to main roads, not streets and highways. I use the Bus Blocker mod to prevent buses to go on certain streets and it also creates bus routes, sort of.
Then on roads that buses traverse but are highly congested by cars, I use UrbanLegends Traffic Controller to create bus and ped only roads (no cars allowed). I use the Road Top Mass Transit mod plus addon pack and Interim Stations to provide stations that don't take up any space at all.
For GLR that is not road-top, I use stations downloaded from the STEX, and for heavy rail I also use stations from the STEX that are appropriate for the location (an urban station would look very different compared to a station in a small farming town).

My red and blue lines cross each other to form a square with stations at each side of the square, then I put a nice park right in the center, or you can put a very high densit building.
The extra stations are somewhat unecessary except for that they provide eye candy, designate a central transit HQ, and since these stations are highly used, they prevent overuse. each side of the tracks provides stops at different locations. For example, if red line track A stops at 15th, 10th, 5th, and Oceanfront Aves, then track B stops at 17th, 12th, 7th, and 2nd Aves. Again this provides a nice look and allows sims to board at more stops without actually adding more stops to a line and thus causing an increase in commute time. It is also an idea to provide bus service at each station, as well as parking garages at your major suburban stops.
By the way, a little warning, do not get carried away with the subway placement. Laying out a subway in a grid pattern with 4-way stops at every block is TERRIBLY unrealistic. The goal is really to cut commute times, provide service to most of your city, and to do so without covering your city in rail. Also, imagine your rail lines as major rivers and bus lines as little creeks. You can't have a thriving river without the little creeks feeding it. So in summary, make bus lines feed each rail station so you can provide widespread transit coverage without spending loads of cash and having rail lines all over the place. To help accomplish that, I can post some links to handy mods if you want.

Never underestimate the power of buses. I used to neglect them due to the space the stops take up, most RL stops are right on the sidewalk. Once I installed RTMT (a transit must-have) and bus stops would be able to be plopped right onto roads without taking up space, I fell in love. Soon, I had plopped bus stops in most congested roads and streets. According to my graph, most Sims walked or took the bus, while a small few drove cars. No congestion whatsoever. Later on, when my city grew a ton, people where starting to prefer cars, and soon they overtook buses in the graph. To fix that, I made a bus mall. I used the Traffic Controller Pack and 3rd and 4th avenues (both were one way streets) in my downtown area bus and ped only. I then placed bus stops two blocks apart. Las ter, I brought the bus system into the suburbs and place stops every four blocks. Then, all was right in my city once more, cars were the minority. I was rolling in mass transit fare dough.
Anyways as far as rail goes, I like to use a little imagination to plot it. I find landmarks or important locations on opposite ends of the map and link them at the city core to make a mass transfer station right downtown. For example I made a two major lines in my city, the Blue Line (to Stadium, Elmonica, via Vertoit City Center/ to Frontier Park Transit Center, Torrington, via Vertoit City Center) and the Red Line (to Airport, Albina, via Vertoit City Center/ to Council Crest TC via Vertoit City Center). The blue line linked my western suburb (Torrington) with my NE suburb Elmonica by going E to W through my city core. My red line connected the airport in the SE suburb of Albina, goes N to S through my city core, and ends at the upscale NW suburb of Council Crest. I then installed the SES (Southern Express Service) which is a passenger rail service (viaduct) that allows commuters to travel along the waterfront at high speeds with a total of three stops.
Torrington--------------------------------------------Vertoit City Center----------------------------------------------------------Albina/ Airport
|-----------------------------------------------------------------|--------------------------------------------------------------------------------|
After that system, I develepod my inter-regional transit. I used undergorund rail to save space, it runs from the W border and splits off to either go to the north or east border with one stop in the city core.
I personally like to use GLR in my downtown areas because you make a very effective system without taking up space at all, plus it looks great! Out in my suburbs I either extend the GLR through it but have the tracks run off of the street and then use suburban center-platform stations. I also use El train in my suburbs and I avoid subways as much as possible, I like being able to see my transit. I only use subways when I have to tunnel under tall mountains or hills.
As far as station placement goes for GLR, in downtown areas I place them 3-5 blocks apart or at landmarks such as the convention center while in suburbs I place them every 10-15 blocks, same for el train. I have nothing to contribute about monorails because i hate them. They look hideous and unrealistic. They can also be a pain to build.
I build highways in simply the most useful areas I can find where they are garunteed to be used (like through sprawling suburbrs) and link send it through or near the city core.
Hope this helps!